


He’s Gone

by peterstark2816



Series: Phil Coulson’s Lost Son [1]
Category: Agents of S.H.I.E.L.D. (TV), Captain America (Movies), Iron Man (Movies), Spider-Man (Tom Holland Movies), The Avengers (Marvel Movies)
Genre: Gen, SHIELD, Spanking
Language: English
Status: Completed
Published: 2021-03-12
Updated: 2021-03-12
Packaged: 2021-03-19 04:28:05
Rating: Not Rated
Warnings: No Archive Warnings Apply
Chapters: 2
Words: 3,113
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/29993880
Author URL: https://archiveofourown.org/users/peterstark2816/pseuds/peterstark2816
Summary: 11th of November, 2005. Phillip J. Coulson remembers this day perfectly. The day his third son was born. Alan Reid Coulson. He remembers holding his son for the first time, his other children crowded right outside the door, Clint trying to keep them all calm. Of course, Nick, Maria, Bruce, Tony, Steve and Bucky were there too, while Trip, Peter, Jemma and Leo stayed at home with Pepper. He remembers the smile on Melinda’s face, the way she teared up, looking at the little bundle, their youngest son. “I truly am the luckiest man on Earth,” he thought, looking at his son. But things can’t always be good, can they?
Series: Phil Coulson’s Lost Son [1]
Series URL: https://archiveofourown.org/series/2206293
Comments: 2
Kudos: 3





	1. Disclaimer and Characters

**Notes for the Chapter:**

> This is an introduction to the characters. The first work will be up in a couple of hours.

Disclaimer  
This part starts in 2005, then moves on to 2006 and ends in 2019.  
Phil Coulson joined SHIELD in 1998. Phil and Nick are almost brothers in this.  
Captain America is still Steve Rogers, but the whole frozen in ice thing never happened. Bucky was only in HYDRA for a year, and Civil War never happened.  
Grant never betrayed SHIELD.  
The attack on New York (2012) hasn’t happened yet. The Avengers are still a thing, they assembled back in 2011. Thor is off-world and probably will be throughout most of the parts.  
Wanda and Pietro were born into HYDRA, therefore they still have their powers, but were rescued at the age of 4 in 2010 and adopted by Clint. They do not remember much about their time in HYDRA.  
Jemma and Leo were adopted by Bruce in 2001 at the age of two. They know that they were adopted, but they do not remember anything before the adoption. Their biological parents are dead. 

Characters, Relationships and Ages 

https://www.familyecho.com/?p=START&c=azzhp4l4yu&f=968110664779441001  
You can follow this link to see the relationships and birth dates on a family tree.

Phillip J. Coulson- 8th of July, 1973. Married to Melinda May. 5 Kids.  
Melinda Qiaolian May-Coulson- 31st of May, 1974. Married Phil Coulson. 5 kids.  
Clinton (Clint) Barton Coulson- 18th of June, 1989. Biological son of Phil and Melinda.  
Natasha (Nat) Romanoff Coulson- 16th of February, 1991. Biological daughter of Phil and Melinda.  
Grant Ward Coulson- 7th of January, 1997. Biological son of Phil and Melinda.  
Skye Johnson Coulson- 6th of May, 2000. Biological daughter of Phil and Melinda.  
Alan Reid Coulson- 11th of November, 2005. Biological son of Phil and Melinda.  
Pietro Jones Coulson- 9th of March, 2006. Adopted son of Clint. Rescued from HYDRA in 2010.  
Wanda Maximoff Coulson- 9th of March, 2006. Adopted daughter of Clint. Rescued from HYDRA in 2010.  
Nicholas (Nick) Joseph Fury- 4th of July, 1969. 1 Son.  
Antoine Triplett (Trip) Fury- 12th of August, 1996. Biological son of Nick Fury.  
Bruce Davis Banner- 18th of December, 1975. 2 Kids.  
Leopold (Leo) Fitz Banner- 19th of August, 1999. Adopted son of Bruce Banner. Adopted from an orphanage in 2001 at the age of two.  
Jemma Simmons Banner- 9th of September, 1999. Adopted daughter of Bruce Banner. Adopted from an orphanage in 2001 at the age of two.  
Steven (Steve) Grant Rogers- 4th of July, 1974. (Still a supersoldier, but born in the modern times.)  
James Buchannan (Bucky) Barnes- 10th of March, 1973. (Still a supersoldier, but born in the modern times. Only spent a year at HYDRA before being rescued and getting rid of the programming in 2002).  
Maria Elizabeth Hill- 4th of July, 1982.  
Anthony Edward Stark- 29th of May, 1978. Married to Pepper Potts-Stark. 1 Kid.  
Virginia (Pepper) Potts-Stark- 10th of July,1979. Married to Tony Stark. 1 Kid.  
Peter Parker Stark- 27th of August, 2001. Biological son of Tony and Pepper.


	2. Alan Reid Coulson

**Summary for the Chapter:**

> 11th of November, 2005. Phillip J. Coulson remembers this day perfectly. The day his third son was born. Alan Reid Coulson. He remembers holding his son for the first time, his other children crowded right outside the door, Clint trying to keep them all calm. Of course, Nick, Maria, Bruce, Tony, Steve and Bucky were there too, while Trip, Peter, Jemma and Leo stayed at home with Pepper. He remembers the smile on Melinda’s face, the way she teared up, looking at the little bundle, their youngest son. “I truly am the luckiest man on Earth,” he thought, looking at his son. But things can’t always be good, can they?

11th of November, 2005. Phillip J. Coulson remembers this day perfectly. The day his third son was born. Alan Reid Coulson. He remembers holding his son for the first time, his other children crowded right outside the door, his eldest, Clint and Nat, trying to keep them all calm. Of course, Nick, Maria, Bruce, Tony, Steve and Bucky were there too, while Trip, Peter, Jemma and Leo stayed at home with Pepper. He remembers the smile on Melinda’s face, the way she teared up, looking at the little bundle, their youngest son. “I truly am the luckiest man on Earth,” he thought, looking at his son. But things can’t always be good, can they? And things did change. 

Alan was different from his other children. Even when he was really small, he was always quiet, calculating even. Phil remembers his youngest son watching the room on his first birthday, a soft smile on his face. He looked around, always curious, but also silent. Nonetheless, Phil loved his son dearly. As a level 6 SHIELD Agent, he wasn’t home often, but he always made sure to spend time with his kids. Clint, who was 17 by the time Alan turned 1, had just graduated from high school and got into the SHIELD Academy as a legacy kid. Natasha, who was 14, was in her junior year of high school, and a black belt in karate and taekwondo. Grant and Skye were still in primary, although both of them had already decided that they wanted to follow their parents’ career. Life couldn’t be better.

On the 13th of December 2006, shortly after Alan’s first birthday, he disappeared. 

It had started as a good day. The family went out to the mall, wanting to do some shopping. They had divided into two groups, Melinda with Nat, Grant and Skye, and Phil with Alan and Clint. Phil was in the bathroom when he was attacked. When he had gone into the bathroom, he felt like something was off. He was too late. Both him and Clint were shot with tranqs, and there wasn’t much he could do. Upon waking up, his youngest was gone. The camera feed was erased, and not even Tony could decipher it. Alan was simply gone. 

Phil was frantic. Both him and Clint blamed themselves because they couldn’t protect their family member. The family was devastated. They spent months and months doing research, searching for clues and trying to find a hint, the smallest hint, that would point them in the right direction. But he was gone. Disappeared without a trace. No sign. Nonetheless, the family kept on searching, utilizing all of SHIELD’s resources with the help of Nick, but even that wasn’t enough. 

It had been the 25th of July 2007, when Phil got the video from an unknown address. A video of his boy. His Alan. Small. Helpless. In a dark basement. To his surprise, Alan wasn’t crying. He was sitting on the floor, watching the room and his surroundings carefully. He was malnourished, with dark circles under his eyes, wearing a simple black baggy outfit. It pained Phil to see his son like that, his son who was so young and didn't deserve any of this. Behind him was a logo, a logo Phil knew all too well. A skull with six octopus arms. HYDRA.

Phil felt his blood turn cold. HYDRA was known for being ruthless and vicious, and he was terrified of what they would do to his young, innocent son. He couldn't put anything past them. Phil was about to alert the rest of his family when he heard a gun click. Frozen in place, he was paralyzed, watching as a gun slowly came into view, aimed at his boy. And then it happened. A loud bang. The lifeless body of his son dropping to the floor. Blood spilling. And there wasn't a single thing Phil could do to stop it. His son was truly gone. 

Twelve years later. 

*Nick Fury and Phil Coulson are the Co-Directors of SHIELD. Maria Hill is the Deputy Director of SHIELD. Melinda May-Coulson is a Level 8 SHIELD Agent. Clint Barton Coulson and Natasha Romanoff Coulson are Level 7 SHIELD Agents. Grant Ward Coulson and Antoine Triplett Fury are Level 6 SHIELD Agents. Doctor Bruce Banner and Doctor Anthony Stark are Level 7 SHIELD Agents. Leo Fitz Banner and Jemma Simmons Banner are Level 5 SHIELD Agents. Skye Coulson and Peter Stark are cadets in the SHIELD Academy. This takes place in June 2019. *

The Co-Directors of SHIELD, Nick Fury and Phil Coulson, were watching the op from the Hub. A simple HYDRA base storm. Nothing too hard. Of course, it didn't stop the two superiors from worrying. After all, those were their children on the op, fighting their way in. Nick watched carefully as Trip knocked out the HYDRA agent who charged at him with a simple move, wincing when the agent managed to punch his son before fainting. Coulson watched with worry and pride as Clint, Natasha and Grant covered for Trip and acted as a team, his eldest subconsciously trying to protect Grant. 

They had infiltrated the base and were almost done with the collection of the intel when the group was attacked by an assassin.  
"Sir, we have a problem. There is an unknown individual on the scene, and we need backup."  
After requesting backup, the four tried to defend themselves against the vigilante who was causing them a lot of trouble, but it was hard. He was fast, slim, and incredibly skilled in hand to hand combat. He was most likely enhanced as well, as he was way stronger than any human being, proving that by lifting an entire conference table and lunging it with one hand as if it were a feather. Trip had just left to deliver the intel as per the Directors' request, and the Coulsons were doing their best to defend themselves against the unknown individual, who was wearing a mask and a black HYDRA suit. Only his eyes and hair were visible. His eyes were an icy cold blue, devoid of any emotions, although there was something similar about them. All three Coulsons felt like they had seen those eyes before, even momentarily, but shrugged the feeling off as they had to knock the other agent out. 

Easier said than done. He was incredibly agile, and any of their punches, arrows or bullets were dodged. It was only when backup arrived and shot him with an ICER that he was finally down, leaving the three Coulsons out of breath and extremely tired. 

There was something about the enhanced individual that left the three siblings deep in thought. Something about his eyes, about the way he moved, that felt entirely too similar.  
Clint voiced his thoughts first. "Is it just me, or there was something about the unknown agent? It's like-"  
Natasha nodded. "It's like I know him. Something about his eyes, the way he looked at us in a calculating way. And the colour, it's so familiar, just like yours Clint."  
Grant added his own part. "They were just like Dad's eyes."  
The three were interrupted by a voice through the comms. "All agents to report to the Hub for a medical and a debrief. Understood?"  
After a collective "Yes, sir", the agents left the base, thinking about what had happened. 

Phil, who was watching the entire operation through the cameras and listening in through the comms, had his own food for thoughts. The individual caught his attention, not just because he would be a valuable SHIELD asset, but also because there was something about him. He could quite pin it yet, but he knew he was close. Knowing that the asset would be transferred to the Fridge as per protocol, he pulled his ranks on some of the operatives and requested that they transfer the knocked out individual to the Avengers Tower and locked him up in the containment area. 

Fury watched his best friend with curiosity, not knowing what it was about the asset that had caught the Coulsons’ eyes. He himself hadn’t noticed anything special about him, except the fact that he was incredibly skilled in the field and could be a potentially valuable asset to SHIELD, but if Phil noticed something about the agent, he wouldn’t interfere. 

Both Phil and Nick left the offices for the Medical, Phil wanting to speak with his children and Nick wanting to check in on Trip. 

Clint was the first to notice them in the Medical. He smiled and waved his dad and uncle over, trying not to get in the way of the doctor who was stitching his shoulder up. Thankfully, none of the agents were badly injured, Clint would need stitches for the gash on his shoulder, Nat had a cut on her thigh, Grant had sprained his wrist, and Trip had a gunshot graze on his side. 

Phil approached Clint after checking in with the other three.  
“How are you feeling, Agent Coulson?” He asked, sitting down next to his son. At first, addressing his children as agents was weird, but it was a requirement at work. They had gotten quite used to it.  
“I’m feeling alright, sir. The mission was a success, we got the necessary intel and even captured the individual.” Upon mentioning the secret agent, Clint’s eyes glassed over, like he was remembering something. “There was something about the individual, sir. Something… familiar? It’s like I knew him. Or used to know him. And he couldn’t be much older than Grant, not with the way he moved, sir.”  
Phil thought about it for a few moments, before replying, “I felt it too. I ordered to have the individual transferred to the Tower, and he will be assessed by Doctor Cho as well as by Doctor Banner to see how old he is and whether he is injured from the fight. There are strong suspicions that he was brainwashed or under the control of HYDRA in some way, although that is unclear for now.” Standing up, Phil quickly looked over the entire area before his eyes focused back on his eldest. “After the debrief, the Quinjet will take you, Agent Coulson, Agent Coulson and Agent Fury to the Tower, Director Fury and I will be there shortly after you. Is that clear?”  
Clint nodded immediately. “Yes, sir.”  
“Alright.” As Phil was heading out of the Medical, he muttered, “And I should really find a new way to address all of you at work.”  
Having heard him, Clint responded, “Sir, you could use our middle names.”  
Phil just nodded and continued his way out of the Medical. 

It hadn’t taken long for all of the Coulsons to meet back at the tower, with the exception of Melinda and Skye, the former of which was on a mission and the latter of which was at the SHIELD Academy. They had all met at the family floor, and then after the short meal, headed to the medical floor where the agents met a surprised Doctor Cho, the individual laying on one of the beds, still unconscious. There were 3 SHIELD Agents positioned next to him, all three looking dishevelled and tired, two of them nursing a sore arm. It was clear that they had to hold the asset down at least once. 

What was more surprising was how young the asset looked. Without the mask and asleep he looked more like a high school student than a deadly and vicious HYDRA soldier. What struck the Coulsons the most was how he looked like a younger version of Clint and Phil. His hair was the same colour as Clint’s, and he looked exactly like Phil did when he was 17. The kid himself couldn’t have been more than 16 years old, although he was in top physical form. Phil heard Grant hold in a gasp beside him, and Natasha looked away. Clint, on the other hand, took a step closer to the teen, stopping a few feet away. Phil’s heart broke for the kid. For a teen to be that good at hand to hand combat, he’d have had to train under HYDRA throughout his entire childhood. This meant that the kid was either born into HYDRA or kidnapped at a very young age. In any case, it meant that he was either severely brainwashed or there against his will. 

Doctor Cho immediately approached the Director and his children. “Phil, Clint, Nat, Grant, welcome.” She acknowledged the entire family before turning to the oldest Coulson. “Phil, there are five things you need to know. Firstly, your assumptions were correct. He was brainwashed. He woke up three times since they brought him in here, but he was much calmer the last time he woke up. We managed to break through the brainwashing the second time he woke up, but it is important to note that the brainwashing was only temporary. It seems that HYDRA had him in a simulation of sorts, where he thought he was a part of SHIELD. He is in top physical form as well, although he has some scars, presumably from the different ops he went on as a HYDRA agent. He will most likely cooperate with you after he wakes up this next time, as he is no longer brainwashed. Secondly… Phil, the kid is only thirteen and a half.” 

“WHAT?!” Was the collective response heard from the Coulsons. The kid that had almost defeated two Avengers and highly trained SHIELD Agents and Specialists was THIRTEEN?

“That’s how old Alan would be…” Grant whispered. Clint looked at his younger brother in concern. 

Doctor Cho looked just as concerned, but she continued talking. “Thirdly, the kid is enhanced. He is a super soldier, just like Steve but more… covert? Enhanced metabolism, super strength, enhanced healing abilities, enhanced hearing and sight, better reflexes,” Doctor Cho grimaced before uttering the next part, “the kid makes a perfect soldier…”

There were a few moments of silence after that, before Nat spoke up. “Weren’t there two more things?”

Helen took a deep breath. “Well, yes. The last time the kid woke up, he told us a bit about himself. He is not gullible or naive, don’t be mistaken, but he was conditioned to follow orders, so when one of the agents you sent here ordered him to talk, he did. Anyways, the kid doesn’t remember much apart from HYDRA. He knows that he was there since he was a kid, and the only memory he has that isn’t somehow associated or affiliated with HYDRA is from when he was a baby, and even that is very fuzzy. He has been going on missions since he was seven years old. He grew up in HYDRA, but he never had a name, he was just Asset. He has a lot of knowledge in the medical field, if his words were anything to go by. We do not know much about the rest of his life, but I’ll take a guess here and say that he never went to school, except maybe some undercover missions.” Helen stopped talking again, throwing a nervous glance at the family.

“You said there were five things,” Prompted Grant. “What is the last?”

Helen took a deep breath before continuing. “And, we took his blood when he just came in, and we had to run multiple tests to know that he wasn’t infected, because it is protocol, and we ran a DNA test and-” Helen stopped abruptly, looking at the family.

“And?” Clint nudged her, having his own suspicions about who the mystery teen was.

“And he’s your son, Phil. Alan Reid Coulson.” Finished Helen.

**Author's Note:**

> There will be non-sexual spanking as a disciplinary measure in the next works.


End file.
